The applications you find running at startup are also listed under
[HKEY_LOCAL_MACHINE\software\microsoft\windows\currentversion\RunOnce]
[HKEY_LOCAL_MACHINE\software\microsoft\windows\currentversion\Start]
[HKEY_LOCAL_MACHINE\software\microsoft\windows\currentversion\Run]
[HKEY_LOCAL_MACHINE\software\microsoft\windows\currentversion\Startup]